---
name: "cif_p1"
section: "1"
platform: "linux"
package: "cod-tools"
version: "3.11.0+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cif_p1"
---

# cif\_p1(1)

expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

## NAME

cif\_p1 - expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

## SYNOPSIS

cif\_p1 --options input1.cif input\*.cif

## DESCRIPTION

Expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).

## OPTIONS

\--always-continue\
                   Continue processing and return successful return status\
                   even if errors are diagnosed.

\-c-, --always-die\
                   Stop and return error status if errors are diagnosed.

\-1, --one-datablock-output\
                   Output all molecules and all alternative conformations\
                   to a single output data block.

\-1-, --multiple-datablocks-output\
                   Separate each molecule and each example of an alternative\
                   conformation into a separate data block.

\-c, --covalent-sensitivity\
                   Set a new covalent sensitivity value (default: 0.35).

\--simplify-formula\
                   Simplify chemical formula and output not the whole\
                   P1 cell but only a minimal stoichiometric set of\
                   molecules. Should have the same result as\
                   'cif\_molecule --preserve-stoichiometry'.

\--dont-simplify-formula, --no-simplify-formula\
                   Do not simplify formula, output the whole P1 cell (default).

\--exclude-zero-occupancies\
                   Do not use atoms with 0 occupancies in calculations\
                   (default).

\--dump-atoms\
                   Dump atoms (including symmetry-equivalent) in CIF\
                   format, for inspection with some graphics program.

\--dont-dump-atoms, --no-dump-atoms\
                   Do not dump atoms (default).

\-i, --ignore-bumps\
                   Detect and warn about close atom "bumps" but do not\
                   stop processing.

\--dont-ignore-bumps, --no-ignore-bumps\
                   Stop processing immediately if bumps are detected (default).

\--bump-distance-factor 0.75\
                   A fraction of covalent bond radii sum used to determine\
                   when atoms are too close and are considered a bump.

\--max-polymer-span 4\
                   A span, in +/- unit cells, in which polymeric molecules\
                   (repeating units) will be constructed.

\--max-polymer-atoms 100\
                   A maximum allowed count of polymer example atoms: more\
                   than this amount of symmetry (translational) equivalent\
                   atoms, for each AU atom, will not be written to the output\
                   file:

                  Using --max-polymer-span=0 --max-polymer-atoms=1\
                   essentially switches off the polymer detection.

\--split-disorder-groups, --dont-merge-disorder-groups\
                   Put examples of disorder group conformations into\
                   separate data blocks (default).

\--merge-disorder-groups, --dont-split-disorder-groups\
                   Put all disorder groups into one data block.

\--use-perl-parser\
                   Use development CIF parser written in Perl.

\--use-c-parser\
                   Use faster C/Yacc CIF parser (default).

\--debug\
                   Print some human-readable debug output.

\--no-debug\
                   Suppress any debug output (default).

\--format "%8.6f"\
                   Use the specified format for output coordinate printout.

\--audit\
                   Print audit information to the generated CIF file (default).

\--no-audit\
                   Do not print audit information to the generated CIF file.

\--continue-on-errors\
                   Do not terminate script if errors such as unrecognised\
                   atoms are encountered; the output may be incorrect and\
                   missing some atoms if this option is used!

\--die-on-errors, --dont-continue-on-errors,

\--no-continue-on-errors\
                   Terminate script immediately if errors are raised (default).

\--continue-on-warnings\
                   Do not terminate script if warnings are raised (default).

\--die-on-warnings\
                   Terminate script immediately if warnings are raised.

\--continue-on-notes\
                   Do not terminate script if notes are raised (default).

\--die-on-notes\
                   Terminate script immediately if notes are raised.

\--verbose\
                   Print warning messages in long format.

\--no-verbose\
                   Print warning messages in concise format (default).

\--help, --usage\
                   Output a short usage message (this message) and exit.

\--version\
                   Output version information and exit.

## REPORTING BUGS

Report cif\_p1 bugs using e-mail: cod-bugs@ibt.lt